Multiple sequence alignment - TraesCS3D01G368500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G368500 chr3D 100.000 3306 0 0 1 3306 481741515 481738210 0.000000e+00 6106
1 TraesCS3D01G368500 chr3B 88.624 3402 154 96 1 3271 643858894 643855595 0.000000e+00 3923
2 TraesCS3D01G368500 chr3A 87.560 2074 90 66 864 2849 624943152 624941159 0.000000e+00 2246
3 TraesCS3D01G368500 chr3A 87.393 468 39 8 1 449 624947992 624947526 1.360000e-143 520
4 TraesCS3D01G368500 chr3A 76.364 440 41 35 2883 3304 624941087 624940693 9.430000e-41 178
5 TraesCS3D01G368500 chr3A 83.333 156 11 9 566 706 624947509 624947354 2.680000e-26 130
6 TraesCS3D01G368500 chr1D 87.273 220 25 2 1620 1836 370885335 370885554 7.080000e-62 248
7 TraesCS3D01G368500 chr1B 87.273 220 25 2 1620 1836 494222761 494222980 7.080000e-62 248
8 TraesCS3D01G368500 chr1A 86.878 221 24 4 1620 1836 469645069 469645288 3.300000e-60 243


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G368500 chr3D 481738210 481741515 3305 True 6106 6106 100.000 1 3306 1 chr3D.!!$R1 3305
1 TraesCS3D01G368500 chr3B 643855595 643858894 3299 True 3923 3923 88.624 1 3271 1 chr3B.!!$R1 3270
2 TraesCS3D01G368500 chr3A 624940693 624943152 2459 True 1212 2246 81.962 864 3304 2 chr3A.!!$R1 2440
3 TraesCS3D01G368500 chr3A 624947354 624947992 638 True 325 520 85.363 1 706 2 chr3A.!!$R2 705

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
618 645 0.361847 CGCTGCGCAAAAATTAACCG 59.638 50.0 13.05 0.0 0.00 4.44 F
1265 1317 0.177836 GAAGCTCTTCTCCAGCCTCC 59.822 60.0 2.55 0.0 37.63 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2120 0.395311 TGGAGGAGCTAGTACCACGG 60.395 60.0 9.34 0.0 0.00 4.94 R
3094 3312 0.095762 GCATCAAAGCATTTTGGCGC 59.904 50.0 0.00 0.0 43.11 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 39 7.482474 TCGTTTGATTCGGTATATGTACAGAA 58.518 34.615 15.32 15.32 44.93 3.02
73 80 4.229582 TGGGAGGGTATTAGATGCAGTTTT 59.770 41.667 0.00 0.00 0.00 2.43
74 81 5.430417 TGGGAGGGTATTAGATGCAGTTTTA 59.570 40.000 0.00 0.00 0.00 1.52
81 88 6.918022 GGTATTAGATGCAGTTTTATTGGCAC 59.082 38.462 0.00 0.00 39.34 5.01
89 96 3.974401 CAGTTTTATTGGCACTTCACGTG 59.026 43.478 9.94 9.94 46.58 4.49
102 109 2.278026 TCACGTGTCCATTCGATCAG 57.722 50.000 16.51 0.00 0.00 2.90
119 128 7.996098 TCGATCAGAAAAAGGGTTTATTTCT 57.004 32.000 0.00 0.00 42.49 2.52
261 277 9.751542 AGAATACATATATAGCAGAATAACGCC 57.248 33.333 0.00 0.00 0.00 5.68
279 295 3.066900 ACGCCGATATGATGCTATAGACC 59.933 47.826 3.21 0.00 0.00 3.85
363 385 1.232621 GGAAACGGTACTGTGGTGGC 61.233 60.000 8.42 0.00 0.00 5.01
383 405 4.281688 TGGCTTGGGAAAAGAAAAGATCTG 59.718 41.667 0.00 0.00 38.79 2.90
510 532 0.510359 CAGCAGCAGACTTTCGTCAC 59.490 55.000 0.00 0.00 42.73 3.67
557 579 0.465097 TTTTTACCGCCCGAACCACA 60.465 50.000 0.00 0.00 0.00 4.17
608 635 2.023771 CTCTGAACTCGCTGCGCAA 61.024 57.895 18.65 0.00 0.00 4.85
618 645 0.361847 CGCTGCGCAAAAATTAACCG 59.638 50.000 13.05 0.00 0.00 4.44
747 783 2.445316 CACTGATGACTGATCGACGAC 58.555 52.381 0.00 0.00 33.17 4.34
760 796 1.513373 GACGACGCTCACACGCATA 60.513 57.895 0.00 0.00 36.19 3.14
785 821 4.135153 CGTCGTAGCCTGCTGCCT 62.135 66.667 0.97 0.00 42.71 4.75
786 822 2.510238 GTCGTAGCCTGCTGCCTG 60.510 66.667 0.97 0.00 42.71 4.85
814 850 2.018727 TTCCACACGTACACGCCTGT 62.019 55.000 0.85 0.00 44.43 4.00
815 851 1.593209 CCACACGTACACGCCTGTT 60.593 57.895 0.85 0.00 44.43 3.16
847 883 1.689959 CATTTTCACTTGCACGCTCC 58.310 50.000 0.00 0.00 0.00 4.70
895 931 6.874134 ACGTATAATTATCCTCTTCACATGCC 59.126 38.462 0.00 0.00 0.00 4.40
937 976 1.854743 CGCCTCACTATTCATGTCACG 59.145 52.381 0.00 0.00 0.00 4.35
967 1006 1.153449 CGCCCTCGCCATTTACTGA 60.153 57.895 0.00 0.00 0.00 3.41
1045 1084 1.151668 CAAGCTCCAAGAACTCCACG 58.848 55.000 0.00 0.00 0.00 4.94
1064 1103 1.080230 CACACTCCCAGCTCACTCG 60.080 63.158 0.00 0.00 0.00 4.18
1150 1196 4.969196 CCGTGCGGTGCTCACTGT 62.969 66.667 10.20 0.00 39.81 3.55
1151 1197 2.967076 CGTGCGGTGCTCACTGTT 60.967 61.111 10.20 0.00 39.81 3.16
1152 1198 2.633657 GTGCGGTGCTCACTGTTG 59.366 61.111 10.20 0.00 39.81 3.33
1153 1199 3.279116 TGCGGTGCTCACTGTTGC 61.279 61.111 10.20 5.69 39.81 4.17
1154 1200 4.030452 GCGGTGCTCACTGTTGCC 62.030 66.667 10.20 0.00 39.81 4.52
1155 1201 3.716006 CGGTGCTCACTGTTGCCG 61.716 66.667 0.80 0.00 33.13 5.69
1265 1317 0.177836 GAAGCTCTTCTCCAGCCTCC 59.822 60.000 2.55 0.00 37.63 4.30
1459 1517 4.189188 CTGTACGAGGACCCGGCG 62.189 72.222 0.00 0.00 0.00 6.46
1498 1556 2.420890 GATGAGCCGGAGCAGGAG 59.579 66.667 5.05 0.00 43.56 3.69
1857 1919 2.857498 AGTTCTAGCTACCCTCCTACCA 59.143 50.000 0.00 0.00 0.00 3.25
1941 2021 2.609610 ACGCACCCACCCCAGTAT 60.610 61.111 0.00 0.00 0.00 2.12
1952 2032 3.265995 CCACCCCAGTATTACTCCTGTTT 59.734 47.826 0.00 0.00 0.00 2.83
1953 2033 4.472108 CCACCCCAGTATTACTCCTGTTTA 59.528 45.833 0.00 0.00 0.00 2.01
1954 2034 5.425630 CACCCCAGTATTACTCCTGTTTAC 58.574 45.833 0.00 0.00 0.00 2.01
1991 2071 9.439500 TGTAACCATTAGTGTTGTAATTCCTAC 57.561 33.333 0.00 0.00 0.00 3.18
2028 2115 5.798015 TCGTCAGTCTGTTAACTAGCTAG 57.202 43.478 19.44 19.44 0.00 3.42
2030 2117 4.095185 CGTCAGTCTGTTAACTAGCTAGCT 59.905 45.833 23.12 23.12 0.00 3.32
2031 2118 5.293814 CGTCAGTCTGTTAACTAGCTAGCTA 59.706 44.000 22.85 22.85 0.00 3.32
2032 2119 6.488817 GTCAGTCTGTTAACTAGCTAGCTAC 58.511 44.000 20.67 13.58 0.00 3.58
2033 2120 5.589452 TCAGTCTGTTAACTAGCTAGCTACC 59.411 44.000 20.67 6.22 0.00 3.18
2034 2121 4.888823 AGTCTGTTAACTAGCTAGCTACCC 59.111 45.833 20.67 6.84 0.00 3.69
2035 2122 3.881688 TCTGTTAACTAGCTAGCTACCCG 59.118 47.826 20.67 13.49 0.00 5.28
2036 2123 3.624777 TGTTAACTAGCTAGCTACCCGT 58.375 45.455 20.67 14.15 0.00 5.28
2037 2124 3.379372 TGTTAACTAGCTAGCTACCCGTG 59.621 47.826 20.67 12.78 0.00 4.94
2038 2125 1.400737 AACTAGCTAGCTACCCGTGG 58.599 55.000 20.67 12.07 0.00 4.94
2039 2126 0.258194 ACTAGCTAGCTACCCGTGGT 59.742 55.000 20.67 12.71 40.16 4.16
2040 2127 1.492176 ACTAGCTAGCTACCCGTGGTA 59.508 52.381 20.67 0.00 37.09 3.25
2041 2128 1.878734 CTAGCTAGCTACCCGTGGTAC 59.121 57.143 20.67 0.00 37.09 3.34
2042 2129 0.258194 AGCTAGCTACCCGTGGTACT 59.742 55.000 17.69 5.15 37.09 2.73
2043 2130 1.492176 AGCTAGCTACCCGTGGTACTA 59.508 52.381 17.69 5.83 37.09 1.82
2044 2131 1.878734 GCTAGCTACCCGTGGTACTAG 59.121 57.143 7.70 20.22 39.70 2.57
2125 2218 1.067821 GGCGAGATGGGTCTAGTCTTG 59.932 57.143 0.00 0.00 33.97 3.02
2255 2380 5.900425 TGTTTGTGTTTGTGCATCAAGTAT 58.100 33.333 0.00 0.00 37.35 2.12
2357 2493 1.895020 TACCGACATGCCACTGGACC 61.895 60.000 0.00 0.00 0.00 4.46
2430 2570 7.919091 GTCCTGTCAACTCGTGAAATATATGTA 59.081 37.037 0.00 0.00 38.23 2.29
2479 2639 0.387494 TTCGTTCTCGTGCATGCGTA 60.387 50.000 14.09 0.00 38.33 4.42
2569 2733 1.244019 GCCCGAGGCTGATTTGTGTT 61.244 55.000 7.58 0.00 46.69 3.32
2571 2735 1.611673 CCCGAGGCTGATTTGTGTTCT 60.612 52.381 0.00 0.00 0.00 3.01
2574 2738 1.129437 GAGGCTGATTTGTGTTCTCGC 59.871 52.381 0.00 0.00 0.00 5.03
2575 2739 1.160137 GGCTGATTTGTGTTCTCGCT 58.840 50.000 0.00 0.00 0.00 4.93
2576 2740 1.135859 GGCTGATTTGTGTTCTCGCTG 60.136 52.381 0.00 0.00 0.00 5.18
2577 2741 1.135859 GCTGATTTGTGTTCTCGCTGG 60.136 52.381 0.00 0.00 0.00 4.85
2578 2742 1.466167 CTGATTTGTGTTCTCGCTGGG 59.534 52.381 0.00 0.00 0.00 4.45
2595 2759 4.329545 GTCCGTTGGCTGGCTCCA 62.330 66.667 2.00 0.00 0.00 3.86
2695 2859 3.496337 CCTGGATGAGATTGGAGTGGATG 60.496 52.174 0.00 0.00 0.00 3.51
2738 2902 1.676678 GATCTCGCCACAGTGCCCTA 61.677 60.000 0.00 0.00 0.00 3.53
2739 2903 1.961180 ATCTCGCCACAGTGCCCTAC 61.961 60.000 0.00 0.00 0.00 3.18
2748 2912 2.058675 AGTGCCCTACCACTGTGTC 58.941 57.895 7.08 0.00 44.00 3.67
2833 3004 1.860950 CGTCTCAGCGTATTCATTGGG 59.139 52.381 0.00 0.00 0.00 4.12
2849 3020 5.151454 TCATTGGGGGTAAATTTTCACTGT 58.849 37.500 0.00 0.00 0.00 3.55
2850 3021 6.315714 TCATTGGGGGTAAATTTTCACTGTA 58.684 36.000 0.00 0.00 0.00 2.74
2876 3059 1.483316 CGTGTACGTCTTCTGTTGCA 58.517 50.000 0.00 0.00 34.11 4.08
2878 3061 1.792949 GTGTACGTCTTCTGTTGCAGG 59.207 52.381 0.00 0.00 31.51 4.85
2879 3062 1.684450 TGTACGTCTTCTGTTGCAGGA 59.316 47.619 0.00 0.00 31.51 3.86
2880 3063 2.299013 TGTACGTCTTCTGTTGCAGGAT 59.701 45.455 0.00 0.00 31.51 3.24
2881 3064 3.508402 TGTACGTCTTCTGTTGCAGGATA 59.492 43.478 0.00 0.00 31.51 2.59
2951 3169 4.406001 TCGACGATCGATTCATTAGAGG 57.594 45.455 24.34 0.00 44.82 3.69
2952 3170 3.813724 TCGACGATCGATTCATTAGAGGT 59.186 43.478 24.34 0.00 44.82 3.85
2954 3172 4.613448 CGACGATCGATTCATTAGAGGTTC 59.387 45.833 24.34 2.19 43.74 3.62
2955 3173 5.561145 CGACGATCGATTCATTAGAGGTTCT 60.561 44.000 24.34 0.00 43.74 3.01
2956 3174 5.524284 ACGATCGATTCATTAGAGGTTCTG 58.476 41.667 24.34 0.00 0.00 3.02
2957 3175 5.299531 ACGATCGATTCATTAGAGGTTCTGA 59.700 40.000 24.34 0.00 0.00 3.27
2958 3176 6.015856 ACGATCGATTCATTAGAGGTTCTGAT 60.016 38.462 24.34 0.00 0.00 2.90
2978 3196 0.963355 TTTATGGCGCCACAGGAACC 60.963 55.000 35.50 0.00 0.00 3.62
2979 3197 3.673956 TATGGCGCCACAGGAACCG 62.674 63.158 35.50 0.00 0.00 4.44
2982 3200 3.723348 GCGCCACAGGAACCGAAC 61.723 66.667 0.00 0.00 0.00 3.95
2992 3210 4.684703 CACAGGAACCGAACACTTTACTAG 59.315 45.833 0.00 0.00 0.00 2.57
2995 3213 6.091437 CAGGAACCGAACACTTTACTAGTAG 58.909 44.000 2.23 0.00 34.56 2.57
3017 3235 0.984230 AGTGGCAAGGCTAGCTACAA 59.016 50.000 15.72 0.00 44.71 2.41
3018 3236 1.065854 AGTGGCAAGGCTAGCTACAAG 60.066 52.381 15.72 1.92 44.71 3.16
3019 3237 1.066143 GTGGCAAGGCTAGCTACAAGA 60.066 52.381 15.72 0.00 42.26 3.02
3020 3238 1.839994 TGGCAAGGCTAGCTACAAGAT 59.160 47.619 15.72 0.00 0.00 2.40
3021 3239 3.038280 TGGCAAGGCTAGCTACAAGATA 58.962 45.455 15.72 0.00 0.00 1.98
3022 3240 3.181465 TGGCAAGGCTAGCTACAAGATAC 60.181 47.826 15.72 0.00 0.00 2.24
3023 3241 3.053455 GCAAGGCTAGCTACAAGATACG 58.947 50.000 15.72 0.00 0.00 3.06
3024 3242 3.491104 GCAAGGCTAGCTACAAGATACGT 60.491 47.826 15.72 0.00 0.00 3.57
3025 3243 4.261489 GCAAGGCTAGCTACAAGATACGTA 60.261 45.833 15.72 0.00 0.00 3.57
3026 3244 5.213675 CAAGGCTAGCTACAAGATACGTAC 58.786 45.833 15.72 0.00 0.00 3.67
3027 3245 3.497640 AGGCTAGCTACAAGATACGTACG 59.502 47.826 15.01 15.01 0.00 3.67
3028 3246 3.249559 GGCTAGCTACAAGATACGTACGT 59.750 47.826 25.98 25.98 0.00 3.57
3029 3247 4.209870 GCTAGCTACAAGATACGTACGTG 58.790 47.826 30.25 15.67 0.00 4.49
3030 3248 3.062323 AGCTACAAGATACGTACGTGC 57.938 47.619 30.25 21.01 0.00 5.34
3035 3253 3.961182 ACAAGATACGTACGTGCTATGG 58.039 45.455 30.25 19.36 0.00 2.74
3067 3285 2.413239 GCATGATCGTATTCATTGGCCG 60.413 50.000 0.00 0.00 34.09 6.13
3070 3288 1.798813 GATCGTATTCATTGGCCGTCC 59.201 52.381 0.00 0.00 0.00 4.79
3080 3298 5.766150 TCATTGGCCGTCCATAAATTTAG 57.234 39.130 3.94 0.00 43.05 1.85
3082 3300 5.530915 TCATTGGCCGTCCATAAATTTAGAG 59.469 40.000 3.94 0.00 43.05 2.43
3094 3312 2.420058 ATTTAGAGACCAAAGCCGGG 57.580 50.000 2.18 0.00 0.00 5.73
3104 3322 3.588057 AAAGCCGGGCGCCAAAATG 62.588 57.895 30.85 12.10 38.78 2.32
3130 3348 3.050703 GCTTCGGATTCAAGCGAGA 57.949 52.632 0.00 0.00 37.14 4.04
3131 3349 0.926846 GCTTCGGATTCAAGCGAGAG 59.073 55.000 0.00 0.00 37.14 3.20
3151 3371 6.250739 CGAGAGCAATTTGATTGATTGTTCAG 59.749 38.462 13.50 5.94 43.14 3.02
3162 3382 4.106029 TGATTGTTCAGTACGCTAGACC 57.894 45.455 0.00 0.00 0.00 3.85
3185 3406 1.213430 ACTTTCGACCCCCTGTTTCAA 59.787 47.619 0.00 0.00 0.00 2.69
3188 3409 2.438800 TCGACCCCCTGTTTCAAAAA 57.561 45.000 0.00 0.00 0.00 1.94
3208 3429 6.463995 AAAAATGAGGTCAAGTTAGCAACA 57.536 33.333 0.00 0.00 0.00 3.33
3209 3430 5.695851 AAATGAGGTCAAGTTAGCAACAG 57.304 39.130 0.00 0.00 0.00 3.16
3210 3431 2.494059 TGAGGTCAAGTTAGCAACAGC 58.506 47.619 0.00 0.00 0.00 4.40
3211 3432 2.158827 TGAGGTCAAGTTAGCAACAGCA 60.159 45.455 0.00 0.00 0.00 4.41
3212 3433 2.481952 GAGGTCAAGTTAGCAACAGCAG 59.518 50.000 0.00 0.00 0.00 4.24
3215 3436 3.433615 GGTCAAGTTAGCAACAGCAGTAG 59.566 47.826 0.00 0.00 0.00 2.57
3216 3437 3.067106 TCAAGTTAGCAACAGCAGTAGC 58.933 45.455 0.00 0.00 42.56 3.58
3217 3438 2.807967 CAAGTTAGCAACAGCAGTAGCA 59.192 45.455 0.00 0.00 45.49 3.49
3218 3439 2.693069 AGTTAGCAACAGCAGTAGCAG 58.307 47.619 0.00 0.00 45.49 4.24
3219 3440 2.037772 AGTTAGCAACAGCAGTAGCAGT 59.962 45.455 0.00 0.00 45.49 4.40
3220 3441 3.258372 AGTTAGCAACAGCAGTAGCAGTA 59.742 43.478 0.00 0.00 45.49 2.74
3221 3442 2.086054 AGCAACAGCAGTAGCAGTAC 57.914 50.000 0.00 0.00 45.49 2.73
3222 3443 1.079503 GCAACAGCAGTAGCAGTACC 58.920 55.000 0.00 0.00 45.49 3.34
3241 3469 2.573462 ACCTACCGTGGTACTCAGAGTA 59.427 50.000 6.15 6.15 38.79 2.59
3275 3513 2.260434 GGCAGTAACAGGACGCGA 59.740 61.111 15.93 0.00 0.00 5.87
3291 3529 1.079127 CGACGCAACTGAATCCCCT 60.079 57.895 0.00 0.00 0.00 4.79
3296 3534 0.684479 GCAACTGAATCCCCTTCCCC 60.684 60.000 0.00 0.00 32.49 4.81
3298 3536 1.571773 AACTGAATCCCCTTCCCCCG 61.572 60.000 0.00 0.00 32.49 5.73
3299 3537 3.416880 TGAATCCCCTTCCCCCGC 61.417 66.667 0.00 0.00 32.49 6.13
3301 3539 4.779486 AATCCCCTTCCCCCGCCT 62.779 66.667 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.644318 ACTTCTGTACATATACCGAATCAAAC 57.356 34.615 0.00 0.00 34.98 2.93
16 17 5.889853 ACTGGACTTCTGTACATATACCGAA 59.110 40.000 0.00 0.00 36.27 4.30
81 88 2.600420 CTGATCGAATGGACACGTGAAG 59.400 50.000 25.01 5.04 0.00 3.02
89 96 4.010349 ACCCTTTTTCTGATCGAATGGAC 58.990 43.478 0.00 0.00 0.00 4.02
102 109 4.242475 CCGCCAGAAATAAACCCTTTTTC 58.758 43.478 0.00 0.00 0.00 2.29
119 128 0.313987 CGATCAGTACATAGCCGCCA 59.686 55.000 0.00 0.00 0.00 5.69
302 321 3.077359 AGCAGTACTTGGCTGAACAATC 58.923 45.455 6.90 0.00 39.30 2.67
334 356 4.573607 ACAGTACCGTTTCCTTGAGAAAAC 59.426 41.667 0.00 0.00 45.93 2.43
348 370 1.070786 CAAGCCACCACAGTACCGT 59.929 57.895 0.00 0.00 0.00 4.83
363 385 7.042797 TCAACAGATCTTTTCTTTTCCCAAG 57.957 36.000 0.00 0.00 29.93 3.61
383 405 3.251245 TCTCTGTCGAGTCTCTGTTCAAC 59.749 47.826 0.00 0.00 38.45 3.18
510 532 2.811431 TCTTGTCACGGCTTTGGTAATG 59.189 45.455 0.00 0.00 0.00 1.90
608 635 1.890489 GGACAGTGGGCGGTTAATTTT 59.110 47.619 0.00 0.00 0.00 1.82
618 645 1.598130 GTGTGACTGGACAGTGGGC 60.598 63.158 10.08 0.69 42.66 5.36
706 742 2.408050 CATGGCCGCAAGATACTACTC 58.592 52.381 0.00 0.00 43.02 2.59
707 743 1.541233 GCATGGCCGCAAGATACTACT 60.541 52.381 0.00 0.00 43.02 2.57
708 744 0.868406 GCATGGCCGCAAGATACTAC 59.132 55.000 0.00 0.00 43.02 2.73
709 745 0.467804 TGCATGGCCGCAAGATACTA 59.532 50.000 2.45 0.00 39.45 1.82
710 746 1.097547 GTGCATGGCCGCAAGATACT 61.098 55.000 6.91 0.00 45.14 2.12
711 747 1.097547 AGTGCATGGCCGCAAGATAC 61.098 55.000 6.91 0.00 45.14 2.24
747 783 0.315625 CATTGCTATGCGTGTGAGCG 60.316 55.000 0.00 0.00 39.14 5.03
786 822 4.465512 CGTGTGGAATGCGGCAGC 62.466 66.667 9.25 0.31 45.41 5.25
814 850 0.243365 AAAATGCATGCCGCGAGAAA 59.757 45.000 16.68 0.00 46.97 2.52
815 851 0.179166 GAAAATGCATGCCGCGAGAA 60.179 50.000 16.68 0.00 46.97 2.87
847 883 2.281208 TGGGTGAAAACGAGCCGG 60.281 61.111 0.00 0.00 33.38 6.13
852 888 2.281208 CGGCCTGGGTGAAAACGA 60.281 61.111 0.00 0.00 0.00 3.85
854 890 2.613506 CGTCGGCCTGGGTGAAAAC 61.614 63.158 0.00 0.00 0.00 2.43
921 960 3.696548 AGAGAGCGTGACATGAATAGTGA 59.303 43.478 0.00 0.00 0.00 3.41
926 965 5.078411 AGTAAAGAGAGCGTGACATGAAT 57.922 39.130 0.00 0.00 0.00 2.57
937 976 0.248702 CGAGGGCGAGTAAAGAGAGC 60.249 60.000 0.00 0.00 40.82 4.09
967 1006 0.823769 TGTGAGAGCGTGAGTGAGGT 60.824 55.000 0.00 0.00 0.00 3.85
1045 1084 1.375268 GAGTGAGCTGGGAGTGTGC 60.375 63.158 0.00 0.00 0.00 4.57
1154 1200 4.214383 CTTGCTCGACATGGCGCG 62.214 66.667 18.42 12.43 0.00 6.86
1155 1201 4.527157 GCTTGCTCGACATGGCGC 62.527 66.667 18.42 3.22 0.00 6.53
1265 1317 2.124693 GCAGGGAGGACGAGGAGAG 61.125 68.421 0.00 0.00 0.00 3.20
1482 1540 2.042537 TCTCCTGCTCCGGCTCAT 60.043 61.111 0.00 0.00 39.59 2.90
1483 1541 3.071206 GTCTCCTGCTCCGGCTCA 61.071 66.667 0.00 0.00 39.59 4.26
1484 1542 4.200283 CGTCTCCTGCTCCGGCTC 62.200 72.222 0.00 0.00 39.59 4.70
1872 1934 2.279784 GGCGGCAGCTAGCTACAG 60.280 66.667 18.86 14.14 44.79 2.74
1873 1935 4.207281 CGGCGGCAGCTAGCTACA 62.207 66.667 18.86 0.00 44.79 2.74
1874 1936 4.951963 CCGGCGGCAGCTAGCTAC 62.952 72.222 18.86 12.37 44.79 3.58
1878 1940 4.880537 CTGACCGGCGGCAGCTAG 62.881 72.222 28.71 13.20 44.37 3.42
1941 2021 8.591072 ACAGTAAGCAATAGTAAACAGGAGTAA 58.409 33.333 0.00 0.00 0.00 2.24
1991 2071 1.604278 TGACGATCGATCAGGTGCTAG 59.396 52.381 24.34 8.47 0.00 3.42
2028 2115 0.667453 GAGCTAGTACCACGGGTAGC 59.333 60.000 3.34 5.82 39.02 3.58
2030 2117 0.921896 AGGAGCTAGTACCACGGGTA 59.078 55.000 9.34 0.00 37.09 3.69
2031 2118 0.395448 GAGGAGCTAGTACCACGGGT 60.395 60.000 9.34 1.14 40.16 5.28
2032 2119 1.108132 GGAGGAGCTAGTACCACGGG 61.108 65.000 9.34 0.00 0.00 5.28
2033 2120 0.395311 TGGAGGAGCTAGTACCACGG 60.395 60.000 9.34 0.00 0.00 4.94
2034 2121 1.338337 CATGGAGGAGCTAGTACCACG 59.662 57.143 9.34 0.00 33.38 4.94
2035 2122 2.362717 GACATGGAGGAGCTAGTACCAC 59.637 54.545 0.00 3.92 33.38 4.16
2036 2123 2.667470 GACATGGAGGAGCTAGTACCA 58.333 52.381 0.00 0.00 35.09 3.25
2037 2124 1.964933 GGACATGGAGGAGCTAGTACC 59.035 57.143 0.00 0.00 0.00 3.34
2038 2125 2.667470 TGGACATGGAGGAGCTAGTAC 58.333 52.381 0.00 0.00 0.00 2.73
2039 2126 3.117131 TGATGGACATGGAGGAGCTAGTA 60.117 47.826 0.00 0.00 0.00 1.82
2040 2127 2.324541 GATGGACATGGAGGAGCTAGT 58.675 52.381 0.00 0.00 0.00 2.57
2041 2128 2.036992 GTGATGGACATGGAGGAGCTAG 59.963 54.545 0.00 0.00 0.00 3.42
2042 2129 2.042464 GTGATGGACATGGAGGAGCTA 58.958 52.381 0.00 0.00 0.00 3.32
2043 2130 0.835941 GTGATGGACATGGAGGAGCT 59.164 55.000 0.00 0.00 0.00 4.09
2044 2131 0.835941 AGTGATGGACATGGAGGAGC 59.164 55.000 0.00 0.00 0.00 4.70
2301 2435 8.725148 AGATGAGTGACAATATGTTTCTTCAAC 58.275 33.333 0.00 0.00 35.71 3.18
2316 2450 6.260050 GGTAAAACAGTGAAAGATGAGTGACA 59.740 38.462 0.00 0.00 0.00 3.58
2357 2493 1.516169 GCGGTAAAAATGGCCAGCG 60.516 57.895 13.05 8.83 35.17 5.18
2430 2570 0.468226 ACGTGACAACATGGAGTGGT 59.532 50.000 0.00 0.00 36.99 4.16
2483 2643 1.674322 ACCAACCCATGCACTACGC 60.674 57.895 0.00 0.00 42.89 4.42
2485 2645 1.883021 GCACCAACCCATGCACTAC 59.117 57.895 0.00 0.00 41.65 2.73
2486 2646 1.673993 CGCACCAACCCATGCACTA 60.674 57.895 0.00 0.00 42.17 2.74
2487 2647 2.985282 CGCACCAACCCATGCACT 60.985 61.111 0.00 0.00 42.17 4.40
2523 2683 0.738389 CTTTTGCACCTGGTTCACGT 59.262 50.000 0.00 0.00 0.00 4.49
2569 2733 3.691342 CCAACGGACCCAGCGAGA 61.691 66.667 0.00 0.00 0.00 4.04
2578 2742 4.329545 TGGAGCCAGCCAACGGAC 62.330 66.667 0.00 0.00 34.31 4.79
2603 2767 2.193536 AGTGAAACAACTGGGCGCC 61.194 57.895 21.18 21.18 41.43 6.53
2695 2859 3.430862 TTGATTCGCACGCCTGCC 61.431 61.111 1.92 0.00 40.73 4.85
2738 2902 0.108585 AATGAAGCCGACACAGTGGT 59.891 50.000 5.31 0.00 0.00 4.16
2739 2903 0.518636 CAATGAAGCCGACACAGTGG 59.481 55.000 5.31 0.00 0.00 4.00
2748 2912 3.864686 CCCGACGCAATGAAGCCG 61.865 66.667 0.00 0.00 0.00 5.52
2833 3004 6.183360 CGTAGACGTACAGTGAAAATTTACCC 60.183 42.308 0.00 0.00 34.11 3.69
2866 3049 8.668510 ACAGTATTATTATCCTGCAACAGAAG 57.331 34.615 0.00 0.00 32.44 2.85
2876 3059 6.745474 GCCTGCAGGAACAGTATTATTATCCT 60.745 42.308 37.21 0.00 37.79 3.24
2878 3061 6.148480 CAGCCTGCAGGAACAGTATTATTATC 59.852 42.308 37.21 12.20 35.83 1.75
2879 3062 6.000219 CAGCCTGCAGGAACAGTATTATTAT 59.000 40.000 37.21 0.00 35.83 1.28
2880 3063 5.368145 CAGCCTGCAGGAACAGTATTATTA 58.632 41.667 37.21 0.00 35.83 0.98
2881 3064 4.202441 CAGCCTGCAGGAACAGTATTATT 58.798 43.478 37.21 3.00 35.83 1.40
2913 3126 1.753463 GACCGACCGATCCAGGAGT 60.753 63.158 0.00 0.00 34.73 3.85
2941 3159 7.012327 CGCCATAAAATCAGAACCTCTAATGAA 59.988 37.037 0.00 0.00 0.00 2.57
2942 3160 6.483307 CGCCATAAAATCAGAACCTCTAATGA 59.517 38.462 0.00 0.00 0.00 2.57
2950 3168 1.748493 TGGCGCCATAAAATCAGAACC 59.252 47.619 29.03 0.00 0.00 3.62
2951 3169 2.163412 TGTGGCGCCATAAAATCAGAAC 59.837 45.455 35.23 15.51 0.00 3.01
2952 3170 2.423185 CTGTGGCGCCATAAAATCAGAA 59.577 45.455 35.23 0.19 0.00 3.02
2954 3172 1.066002 CCTGTGGCGCCATAAAATCAG 59.934 52.381 35.23 30.26 0.00 2.90
2955 3173 1.102154 CCTGTGGCGCCATAAAATCA 58.898 50.000 35.23 23.09 0.00 2.57
2956 3174 1.388547 TCCTGTGGCGCCATAAAATC 58.611 50.000 35.23 19.34 0.00 2.17
2957 3175 1.476488 GTTCCTGTGGCGCCATAAAAT 59.524 47.619 35.23 0.00 0.00 1.82
2958 3176 0.885196 GTTCCTGTGGCGCCATAAAA 59.115 50.000 35.23 22.85 0.00 1.52
2978 3196 5.345202 CCACTTGCTACTAGTAAAGTGTTCG 59.655 44.000 28.99 18.56 39.39 3.95
2979 3197 5.120363 GCCACTTGCTACTAGTAAAGTGTTC 59.880 44.000 28.99 21.61 39.39 3.18
2980 3198 4.995487 GCCACTTGCTACTAGTAAAGTGTT 59.005 41.667 28.99 7.84 39.39 3.32
2981 3199 4.039973 TGCCACTTGCTACTAGTAAAGTGT 59.960 41.667 28.99 15.04 42.00 3.55
2982 3200 4.566004 TGCCACTTGCTACTAGTAAAGTG 58.434 43.478 26.77 26.77 42.00 3.16
2992 3210 1.373570 CTAGCCTTGCCACTTGCTAC 58.626 55.000 0.00 0.00 42.00 3.58
2995 3213 0.392998 TAGCTAGCCTTGCCACTTGC 60.393 55.000 12.13 0.00 41.77 4.01
3001 3219 2.629336 ATCTTGTAGCTAGCCTTGCC 57.371 50.000 12.13 0.00 0.00 4.52
3009 3227 3.873361 AGCACGTACGTATCTTGTAGCTA 59.127 43.478 22.34 0.00 0.00 3.32
3017 3235 2.292569 CACCCATAGCACGTACGTATCT 59.707 50.000 22.34 21.51 0.00 1.98
3018 3236 2.033801 ACACCCATAGCACGTACGTATC 59.966 50.000 22.34 15.55 0.00 2.24
3019 3237 2.026641 ACACCCATAGCACGTACGTAT 58.973 47.619 22.34 15.14 0.00 3.06
3020 3238 1.401552 GACACCCATAGCACGTACGTA 59.598 52.381 22.34 6.15 0.00 3.57
3021 3239 0.171903 GACACCCATAGCACGTACGT 59.828 55.000 16.72 16.72 0.00 3.57
3022 3240 0.171679 TGACACCCATAGCACGTACG 59.828 55.000 15.01 15.01 0.00 3.67
3023 3241 2.373540 TTGACACCCATAGCACGTAC 57.626 50.000 0.00 0.00 0.00 3.67
3024 3242 3.620427 ATTTGACACCCATAGCACGTA 57.380 42.857 0.00 0.00 0.00 3.57
3025 3243 2.487762 CAATTTGACACCCATAGCACGT 59.512 45.455 0.00 0.00 0.00 4.49
3026 3244 2.731968 GCAATTTGACACCCATAGCACG 60.732 50.000 0.00 0.00 0.00 5.34
3027 3245 2.230992 TGCAATTTGACACCCATAGCAC 59.769 45.455 0.00 0.00 0.00 4.40
3028 3246 2.523245 TGCAATTTGACACCCATAGCA 58.477 42.857 0.00 0.00 0.00 3.49
3029 3247 3.130869 TCATGCAATTTGACACCCATAGC 59.869 43.478 0.00 0.00 0.00 2.97
3030 3248 4.987408 TCATGCAATTTGACACCCATAG 57.013 40.909 0.00 0.00 0.00 2.23
3035 3253 3.492421 ACGATCATGCAATTTGACACC 57.508 42.857 0.00 0.00 0.00 4.16
3067 3285 6.458342 CGGCTTTGGTCTCTAAATTTATGGAC 60.458 42.308 16.10 16.10 0.00 4.02
3070 3288 5.221048 CCCGGCTTTGGTCTCTAAATTTATG 60.221 44.000 0.00 0.00 0.00 1.90
3094 3312 0.095762 GCATCAAAGCATTTTGGCGC 59.904 50.000 0.00 0.00 43.11 6.53
3104 3322 3.432782 CTTGAATCCGAAGCATCAAAGC 58.567 45.455 0.00 0.00 31.94 3.51
3130 3348 6.803320 CGTACTGAACAATCAATCAAATTGCT 59.197 34.615 0.00 0.00 40.05 3.91
3131 3349 6.452872 GCGTACTGAACAATCAATCAAATTGC 60.453 38.462 0.00 0.00 40.05 3.56
3132 3350 6.803320 AGCGTACTGAACAATCAATCAAATTG 59.197 34.615 0.00 0.00 41.57 2.32
3134 3352 6.500684 AGCGTACTGAACAATCAATCAAAT 57.499 33.333 0.00 0.00 34.49 2.32
3135 3353 5.940192 AGCGTACTGAACAATCAATCAAA 57.060 34.783 0.00 0.00 34.49 2.69
3136 3354 6.310467 GTCTAGCGTACTGAACAATCAATCAA 59.690 38.462 0.00 0.00 34.49 2.57
3137 3355 5.805486 GTCTAGCGTACTGAACAATCAATCA 59.195 40.000 0.00 0.00 34.49 2.57
3138 3356 5.232414 GGTCTAGCGTACTGAACAATCAATC 59.768 44.000 0.00 0.00 34.49 2.67
3151 3371 3.363128 GTCGAAAGTTTGGTCTAGCGTAC 59.637 47.826 0.00 0.00 0.00 3.67
3162 3382 1.687563 AACAGGGGGTCGAAAGTTTG 58.312 50.000 0.00 0.00 0.00 2.93
3185 3406 6.463995 TGTTGCTAACTTGACCTCATTTTT 57.536 33.333 0.00 0.00 0.00 1.94
3188 3409 3.503748 GCTGTTGCTAACTTGACCTCATT 59.496 43.478 0.00 0.00 36.03 2.57
3195 3416 3.067106 GCTACTGCTGTTGCTAACTTGA 58.933 45.455 19.71 0.00 40.73 3.02
3198 3419 2.037772 ACTGCTACTGCTGTTGCTAACT 59.962 45.455 25.06 7.40 46.76 2.24
3199 3420 2.417719 ACTGCTACTGCTGTTGCTAAC 58.582 47.619 25.06 3.41 46.76 2.34
3201 3422 2.094182 GGTACTGCTACTGCTGTTGCTA 60.094 50.000 25.06 11.75 46.76 3.49
3202 3423 1.338200 GGTACTGCTACTGCTGTTGCT 60.338 52.381 25.06 12.59 46.76 3.91
3204 3425 2.751166 AGGTACTGCTACTGCTGTTG 57.249 50.000 0.09 0.58 46.76 3.33
3205 3426 2.496470 GGTAGGTACTGCTACTGCTGTT 59.504 50.000 0.09 0.00 46.76 3.16
3207 3428 1.065701 CGGTAGGTACTGCTACTGCTG 59.934 57.143 8.59 0.00 42.03 4.41
3208 3429 1.340795 ACGGTAGGTACTGCTACTGCT 60.341 52.381 14.58 3.98 42.03 4.24
3209 3430 1.101331 ACGGTAGGTACTGCTACTGC 58.899 55.000 14.58 0.00 42.03 4.40
3210 3431 1.404391 CCACGGTAGGTACTGCTACTG 59.596 57.143 13.56 13.56 42.03 2.74
3211 3432 1.005215 ACCACGGTAGGTACTGCTACT 59.995 52.381 8.59 0.00 42.03 2.57
3212 3433 1.467920 ACCACGGTAGGTACTGCTAC 58.532 55.000 0.00 0.00 42.03 3.58
3219 3440 2.573462 ACTCTGAGTACCACGGTAGGTA 59.427 50.000 8.91 5.67 43.08 3.08
3220 3441 1.353694 ACTCTGAGTACCACGGTAGGT 59.646 52.381 8.91 7.29 45.72 3.08
3221 3442 2.125773 ACTCTGAGTACCACGGTAGG 57.874 55.000 8.91 0.00 0.00 3.18
3275 3513 0.322546 GGAAGGGGATTCAGTTGCGT 60.323 55.000 0.00 0.00 39.91 5.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.